As you would expect, there was a wave -- totally justified -- of press coverage of the major speech that was delivered by President Barack Obama during his return to Jakarta, Indonesia, a city that he called home as a child. To read the speech text, click here.
All of the major stories focused on the same core theme -- Obama's praise for Indonesia's rich history of religious tolerance, especially in the context of the wider Muslim world. Thus, in the New York Times one could read the following passage:

Mixing the personal, political and religious, Mr. Obama spoke of Indonesia's history of religious tolerance and its commitment to democracy and diversity before a receptive audience of 6,500 mostly young people at the University of Indonesia. In a 30-minute speech, the president underscored the shared values between the United States and Indonesia, which is known for its tradition of moderate Islam.

Mr. Obama spoke about hearing the "call to prayer across Jakarta," where he lived for four years as a boy. He referred several times to his Indonesian stepfather, Lolo Soeotoro, who, he said, "was raised a Muslim" but "firmly believed that all religions were worthy of respect."

"I thought the speech was very good because it showed that Obama knows about the people of Indonesia, our cultures and traditions, and mentioned what we have in common," said Slamet Effendi Yusuf, a deputy chairman of Nahdlatul Ulama, one of Indonesia's largest Islamic organizations. "He was arguing against the people who say that there is something incompatible between Islamic and Christian civilizations."

Although 90 percent of Indonesia's nearly 240 million citizens are Muslim, the country's constitution recognizes the world's major religions, and for decades political Islam had little role in this country. But in the past two decades, as Indonesians have become increasingly religious, events in the Middle East and other Muslim regions have gained more traction here.

That last sentence is absolutely crucial and I'll return to it shortly.

However, you could see some of the same essential issues covered in the following slice of the Washington Postreport on the same subject:

(Obama) also praised Indonesia -- the world's most populous Muslim-majority nation -- for a "spirit of tolerance that is written into your constitution, symbolized in your mosques and churches and temples, and embodied in your people," a quality worthy for all the world to emulate.

Obama received a warm welcome from the crowd of about 6,500 at the University of Indonesia, particularly when he spoke in Indonesian, as when he recalled buying satay and bakso from street vendors or referenced the national motto, "Bhinneka Tunggal Ika," or "Unity in Diversity."

"We are two nations which have traveled different paths. Yet our nations show that hundreds of millions who hold different beliefs can be united in freedom under one flag," Obama said.

Now, stop and think about this.

Did you notice the following phrase in that New York Times piece? It seems that life has become more complex -- the hint is that the emphasis in tolerance has changed somehow -- in the "past two decades, as Indonesians have become increasingly religious."

That's the phrase that made me think of the following, which is the top of a Scripps Howard News Service column that I wrote more than a decade ago -- months before the events of Sept. 11, in fact. The setting, of course, is Indonesia:

One wave of warriors came out of the mountains while another came in boats from the sea, crushing the harbor villages on the island of Haruku.

"I heard a grenade and the house went up in an explosion at about 5:30 a.m.," said an Indonesian pastor, in testimony read in the British House of Lords. "Nine people died at the football pitch. ... Some were injured, but still alive, when the military came with bayonets and stabbed them in the neck."

Similar attacks have destroyed hundreds of churches and mosques during the past two years in the Maluku Islands, which were once known as the romantic "Spice Islands."

"Those who died were beheaded," he said. "We have not been able to find their heads, because the soldiers take them."

Hacking off the heads makes it harder to identify victims in the jungles far from modern Indonesia's cities. Witnesses say the raiders wear white jihad robes, often over military uniforms.

The material made it into the House of Lords and, thus, the public record, because of the work of a controversial human-rights activist, the nurse and sociologist Baroness Caroline Cox. The key, she said, is that some people believe that it is impossible to stand up and defend universal human rights -- such as the freedom of religious conscience -- because these concepts are said to be the products of the Judeo-Christian West.

in Indonesia, some of the people who were fighting and dying to protect those freedoms were -- yes, emphasize this -- Muslims. Churches were destroyed. So were some selected mosques.

... (The) Indonesia crisis is not a simple clash between Islam and Christianity. Cox said she has seen evidence of Muslims dying to defend the homes and churches of neighbors.

The Republic of Indonesia is stunningly complex, a 3,500-mile crescent of 17,670 islands straddling the equinox between the Indian and Pacific oceans. The world's largest archipelago is nearly three times the size of Texas and the population of 225 million includes 300 ethnic groups. The population of 225 million is 88 percent Muslim and 8 percent Christian, with smaller communities of Hindus, Buddhists and others.

I left that last paragraph in for a reason. Clearly, the journalists covering the Obama visit to Indonesia -- and writing about its legitimate heritage of a limited tolerance of minority religions -- could not go into these issues in depth.

But, GetReligion readers, did anyone see any mainstream coverage that mentioned that this nation's heritage of tolerance is under violent attack? Did anyone read about the "white riders"? About kidnappings? Beheadings? The persecution and killing of, for lack of a better word, "moderate" Muslims, as well as members of religious minorities?

And what did the Times report really mean when it said that these problems are in the rise because "Indonesians have become increasingly religious"? Isn't that a haunting statement to accept as fact?

So Muslims who are more religious are violent. Those who are less religious are tolerant. And note that it is "political Islam" that is the problem, yet this "political Islam" comes to power when people become "increasingly religious." Is that what the editors meant to say?